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X-ray phase tomography aims at reconstructing the 3D electron density distribution of an object. It offers enhanced sensitivity compared to attenuation-based X-ray absorption tomography. In propagation-based methods, phase contrast is achieved by letting the beam propagate after interaction with the object. The phase shift is then retrieved at each projection angle, and subsequently used in tomographic reconstruction to obtain the refractive index decrement distribution, which is proportional to the electron density. Accurate phase retrieval is achieved by combining images at different propagation distances. For reconstructions of good quality, the phase-contrast images recorded at different distances need to be accurately aligned. In this work, we characterise the artefacts related to misalignment of the phase-contrast images, and investigate the use of different registration algorithms for aligning in-line phase-contrast images. The characterisation of artefacts is done by a simulation study and comparison with experimental data. Loss in resolution due to vibrations is found to be comparable to attenuation-based computed tomography. Further, it is shown that registration of phase-contrast images is nontrivial due to the difference in contrast between the different images, and the often periodical artefacts present in the phase-contrast images if multilayer X-ray optics are used. To address this, we compared two registration algorithms for aligning phase-contrast images acquired by magnified X-ray nanotomography: one based on cross-correlation and one based on mutual information. We found that the mutual information-based registration algorithm was more robust than a correlation-based method.

Modern breeding of sunflower (Helianthus annuus L.), which started 100 years ago, increased the number and the diversity of cultivated forms. In addition, for more than 50 years, wild sunflower and other Helianthus species have been collected in North America where they all originated. Collections of both cultivated and wild forms are maintained in gene banks in many countries where sunflower is an important crop, with some specificity according to the availability of germplasm and to local research and breeding programmes. Cultivated material includes land races, open pollinated varieties, synthetics and inbred lines. The majority of wild accessions are ecotypes of wild Helianthus annuus, but also 52 other species of Helianthus and a few related genera. The activities of three gene banks, in USA, France and Serbia, are described in detail, supplemented by data from seven other countries. Past and future uses of the genetic resources for environmental adaptation and breeding are discussed in relation to genomic and improved phenotypic knowledge of the cultivated and wild accessions available in the gene banks. L’amélioration moderne du tournesol (Helianthus annuus L.) a débuté il y a un siècle, diversifiant et augmentant le nombre des formes cultivées du tournesol. De plus, des collectes de tournesols sauvages et d’espèces du genre Helianthus ont lieu depuis 50 ans en Amérique du Nord d’où ils sont tous originaires. Ainsi, des collections de tournesols cultivés et sauvages sont conservées par des centres de ressources génétiques dans de nombreux pays où le tournesol est une culture importante. Chacun d’eux présente des spécificités par rapport aux ressources génétiques maintenues, en fonction des programmes de recherche ou de sélection variétale locales. Le matériel génétique cultivé comprend des écotypes, des populations et des lignées tandis que les accessions sauvages correspondent eux écotypes d’Helianthus annuus sauvages et des 52 autres espèces apparentées du genre Helianthus. Les activités de trois centres de ressources génétiques des États-Unis, de la France et de la Serbie sont décrites en détail, complétées par des données provenant des centres de sept autres pays. L’historique de l’utilisation des ressources génétiques et les perspectives futures pour l’adaptation des variétés à l’environnement sont discutés ainsi que leur caractérisation au niveau génomique et phénotypique. The Supplementary Material is available at [https://www.ocljournal.org/10.1051/ocl/2020004/olm].

The current work was conducted to investigate the effectiveness of two conceptually distinct in silico ligand-based tools: Partial Least Squares Discriminant Analysis (PLS-DA) and 3D similarity, including shape, physico-chemical and electrostatics to classify target-specific pharmacophores with enrichment power for selective GSK-3 inhibitors against the phylogenetically related CDK-2, CDK-4, CDK-5 and PKC. All virtual screens were performed on four data sets of targets matched pairwise, including selective and nonselective inhibitors for GSK-3. The classification method PLS-DA results revealed that all obtained models are statistically robust according to the cross-validation and response permutation tests. Regarding selective GSK-3 inhibitors differentiation in terms of selectivity (Se), specificity (Sp), and accuracy (ACC), the PLS-DA models for CDK-4/GSK-3, and PKC/GSK-3 datasets are highly efficient discriminative. 3D similarity searches for CDK-4/GSK-3, PKC/GSK-3, and CDK-2/GSK-3 datasets using the most selective reference molecules lead to highest enrichments of selective GSK-3 inhibitors. EON yields excellent early and overall enrichments for ET_ST and ET_combo for most selective query for CDK-4/GSK-3. CDK-5/GSK-3 dataset didn't show consistent statistically significant enrichments for 3D similarity virtual screening. The current methodology is reliable and could be used as a powerful tool for the detection of potentially selective molecules targeting GSK-3.

Significance Silver nanowires are a type of novel fiber that are likely to have wide application in consumer electronics but that can also carry risk for cell internalization and toxicity. Here, we show that silver nanowire toxicity can be greatly diminished by reducing nanowire diameter without affecting device performance. X-ray microscopy and supporting studies revealed that endolysosome membranes can mechanically crumple thin silver nanowires, the likely mechanism for diminishing toxicity., Fibrous particles interact with cells and organisms in complex ways that can lead to cellular dysfunction, cell death, inflammation, and disease. The development of conductive transparent networks (CTNs) composed of metallic silver nanowires (AgNWs) for flexible touchscreen displays raises new possibilities for the intimate contact between novel fibers and human skin. Here, we report that a material property, nanowire-bending stiffness that is a function of diameter, controls the cytotoxicity of AgNWs to nonimmune cells from humans, mice, and fish without deterioration of critical CTN performance parameters: electrical conductivity and optical transparency. Both 30- and 90-nm-diameter AgNWs are readily internalized by cells, but thinner NWs are mechanically crumpled by the forces imposed during or after endocytosis, while thicker nanowires puncture the enclosing membrane and release silver ions and lysosomal contents to the cytoplasm, thereby initiating oxidative stress. This finding extends the fiber pathology paradigm and will enable the manufacture of safer products incorporating AgNWs.

The osteocyte lacuno-canalicular network (LCN) is essential for bone remodeling because osteocytes regulate cell recruitment. This has been proposed to occur through liquid-flow-induced shear forces in the canaliculi. Models of the LCN have thus far assumed that it contains canaliculi connecting the osteocyte lacunae. However, here, we reveal that enlarged spaces occur at places where several canaliculi cross; we name these spaces canalicular junctions. We characterize them in detail within mice cortical bone using synchrotron nanotomography at two length scales, with 50 and 130 nm voxel size, and show that canalicular junctions occur at a density similar to that of osteocyte lacunae and that canalicular junctions tend to cluster. Through confocal laser scanning microscopy, we show that canalicular junctions are widespread as we have observed them in cortical bone from several species, even though the number density of the canalicular junctions was not universal. Fluid flow simulations of a simple model system with and without a canalicular junction clearly show that liquid mass transport and flow velocities are altered by the presence of canalicular junctions. We suggest that these canalicular junctions may play an important role in osteocyte communication and possibly also in canalicular fluid flow. Therefore, we believe that they constitute an important component in the bone osteocyte network.

Three-dimensional (3D) nanostructures are drawing a fast-growing attention for their advanced functionalities in nanophotonics [1], photovoltaics, and novel 3D integrated circuits and flash memories. The functionalities of such nanostructures are fundamentally determined by their complex internal structure. Inevitably, any fabricated nanostructure differs from its initial design. Hence, the observed functionality differs from the expected one. It is thus critical to assess the structure of a 3D nanomaterial and verify how well it matches the design. Ideally such an inspection technique leaves no traces of the inspection in order to leave the nanostructure fully functional and ready for integration. Here, we introduce traceless X-ray tomography (TXT) as a new methodology in nanotechnology to non-destructively assess the functionality of nanostructures.

It is a major outstanding goal in Nanophotonics to precisely place quantum emitters inside a three-dimensional (3D) metamaterial. It is well-known that such control offers exquisite control over cavity QED, spontaneous and stimulated emission, and even non-linear optics [1]. Theory predicts that the emission of an emitter, e.g. a quantum dot, varies spatially on 100s nm scale [2]. Thus, the challenge is to place emitters with a precision better than Δx < 100 nm. We present our newly developed chemical toolbox to fix the positions of quantum dots with a polymer brush layer with thicknesses in the 10s nm range in silicon nanostructures [3].

Elucidating the structure of neuronal networks provides a foundation for understanding how the nervous system processes information to generate behavior. Despite technological breakthroughs in visible light and electron microscopy, imaging dense nanometer-scale neuronal structures over millimeter-scale tissue volumes remains a challenge. Here, we demonstrate that X-ray holographic nano-tomography is capable of imaging large tissue volumes with sufficient resolution to disentangle dense neuronal circuitry in Drosophila melanogaster and mammalian central and peripheral nervous tissue. Furthermore, we show that automatic segmentation using convolutional neural networks enables rapid extraction of neuronal morphologies from these volumetric datasets. The technique we present allows rapid data collection and analysis of multiple specimens, and can be used correlatively with light microscopy and electron microscopy on the same samples. Thus, X-ray holographic nano-tomography provides a new avenue for discoveries in neuroscience and life sciences in general.

International audience; We have recently developed a series of tamoxifen-like metallocifens of the group-8 metals (Fe, Ru and Os) with strong antiproliferative activity on the triple negative breast cancer cells (MDA-MB-231). This property, not observed for the organic analog 4-hydroxytamoxifen, has been associated with the unique redox behavior of metallocenic moieties, readily affording reactive quinone methides in cancer cells. To shed light on the mechanism of action of these molecules, synchrotron radiation X-ray fluorescence (SR-XRF) nanoimaging studies were performed on cells exposed to osmocenyltamoxifen (Oc-OH-Tam) to disclose its intracellular distribution using osmium as an intrinsic reporter. High resolution mapping of the lipophilic Oc-OH-Tam in cells, revealed its preferential accumulation in the endomembrane system encompassing endoplasmic reticulum,nuclear envelope and vesicular structures. This is consistent with the ability of the amino nitrogen chain of the compounds to be protonated at physiological pH and responsible for electrostatic interactions between Oc-OH-Tam and membranes. We propose a comprehensive scenario that provides new insight into the cellular behavior and activation of Oc-OH-Tam and advances the understanding of its mechanism of action.

The degenerative effects of multiple sclerosis at the level of the vascular and neuronal networks in the central nervous system are currently the object of intensive investigation. Preclinical studies have demonstrated the efficacy of mesenchymal stem cell (MSC) therapy in experimental autoimmune encephalomyelitis (EAE), the animal model for multiple sclerosis, but the neuropathology of specific lesions in EAE and the effects of MSC treatment are under debate. Because conventional imaging techniques entail protocols that alter the tissues, limiting the reliability of the results, we have used non-invasive X-ray phase-contrast tomography to obtain an unprecedented direct 3D characterization of EAE lesions at micro-to-nano scales, with simultaneous imaging of the vascular and neuronal networks. We reveal EAE-mediated alterations down to the capillary network. Our findings shed light on how the disease and MSC treatment affect the tissues, and promote X-ray phase-contrast tomography as a powerful tool for studying neurovascular diseases and monitoring advanced therapies.

We present here a correlative X-ray microscopy approach for quantitative single cell imaging of molar concentrations. By combining the elemental content provided by X-ray fluorescence microscopy and the morphology information extracted from X-ray phase nanotomography, we determine the intracellular molarity distributions. This correlative method was demonstrated on a freeze-dried human phagocytic cell to obtain the absolute elemental concentration maps of K, P, and Fe. The cell morphology results showed a very good agreement with atomic-force microscopy measurements. This work opens the way for non-destructive single cell chemical analysis down to the sub-cellular level using exclusively synchrotron radiation techniques. It will be of high interest in the case where it is difficult to access the morphology using atomic-force microscopy, for example, on frozen-hydrated cells or tissues.

International audience; Newly available x-ray nanobeams in synchrotron radiation facilities open new research avenues in the nanosciences. However, a significant challenge is to efficiently concentrate, particularly for high-energy x-rays, a large photon flux into a very small focal spot. Here, we demonstrate for the first time, to the best of our knowledge, a sub-13-nm (FWHM) diffraction-limited x-ray focus size with 6 billion photons per second formed using elliptically figured mirrors operating at 33.6 keV. This is the smallest and brightest focus spot in this high-energy range. We report the results of an x-ray ptychography experiment to characterize the wavefront at the focus position. This offers new opportunities in multidisciplinary fields for x-ray microscopy techniques in which the focal spot size limits the resolution. (C) 2017 Optical Society of America

The last decades were beneficial for nanofabrication techniques but validation of the increasingly complex nano-structures became more challenging. Recent advancements of X-ray tomography permit 3D reconstruction down to 20 nm resolution. We propose the use of this non-invasive technique to quantify the fabrication quality of 3D structures made with direct laser writing (DLW). The comparison of X-ray density function with the designed fabrication density map brings into light information of how polymerization takes place throughout the fabricated volume and also gives the opportunity to estimate the impact on the optical response of such media.

In propagation based phase contrast imaging, intensity patterns are recorded on a x-ray detector at one or multiple propagation distances, called in-line holograms. They form the input of an inversion algorithm that aims at retrieving the phase shift induced by the object. The problem of phase retrieval in in-line holography is an ill-posed inverse problem. Consequently an adequate solution requires some form of regularization with the most commonly applied being the classical Tikhonov regularization. While generally satisfying this method suffers from a few issues such as the choice of the regularization parameter. Here, we offer an alternative to the established method by applying the principles of Bayesian inference. We construct an iterative optimization algorithm capable of both retrieving the unknown phase and determining a multi-dimensional regularization parameter. In the end, we highlight the advantages of the introduced algorithm, chief among them being the unsupervised determination of the regularization parameter(s). The proposed approach is tested on both simulated and experimental data and is found to provide robust solutions, with improved response to typical issues like low frequency noise and the twin-image problem.

International audience; X-ray ptychography is a coherent diffraction imaging technique with a high resolving power and excellent quantitative capabilities. Although very popular in synchrotron facilities nowadays, its implementation with X-ray energies above 15 keV is very rare due to the challenges imposed by the high energies. Here, the implementation of high-energy X-ray ptychography at 17 and 33.6 keV is demonstrated and solutions to overcome the important challenges are provided. Among the particular aspects addressed are the use of an efficient high-energy detector, a long synchrotron beamline for the high degree of spatial coherence, a beam with 1% monochromaticity providing high flux, and efficient multilayer coated Kirkpatrick-Baez X-ray optics to shape the beam. The constraints imposed by the large energy bandwidth are carefully analyzed, as well as the requirements to sample correctly the high-energy diffraction patterns with small speckle size. In this context, optimized scanning trajectories allow the total acquisition time to be reduced by up to 35%. The paper explores these innovative solutions at the ID16A nano-imaging beamline by ptychographic imaging of a 200 nm-thick gold lithography sample.

International audience

Enabling exploration of biological tissue in three-dimensions at sub-cellular scale is instrumental for advancing our understanding of biological systems and for finding better ways to cope with diseases. Over the last few years, remarkable advances in microscopy facilitated probing cells and tissues at the nanometer scale but many limitations are yet to be overcome. Here we present a novel technique which enables label-free volume imaging of biological tissue with pixel sizes down to 25 nm while maintaining extensive sample coverage. X-ray holographic nanotomography is a full-field 3D imaging technique which benefits from the deep penetration of X-rays and the powerful mechanism of phase contrast. By using cryogenic sample preservation, the tissue can be investigated close to the native state. The unprecedented data created by this technique opens new avenues in life sciences research.

ZusammenfassungGesunder humaner Knochen unterliegt einem permanenten Umbau, um sich den mechanischen Anforderungen anzupassen, Mikrofrakturen zu reparieren und das Mineralgleichgewicht zu erhalten. Der Umbauprozess der extrazellulären Matrix wird durch Osteoblasten und Osteoklasten realisiert. Eine bedeutende Rolle bei der Regulierung der Osteoklasten- und Osteoblastenaktivität wird den Osteozyten zugesprochen, welche in einem komplexen Netzwerk von Zelllakunen und Kanalikuli die extrazelluläre Matrix durchsetzen. Auf Phasenkontrast basierende hochauflösende Nano-Computertomografie erlaubt erstmals, sowohl das Zellnetzwerk als auch die direkt angrenzende mineralisierte Matrix in Untersuchungsvolumen, die hinsichtlich ihrer Größe als repräsentativ angesehen werden können, im nativen Zustand (nicht demineralisiert, nicht eingebettet) zu untersuchen.

A reliability analysis attempt is hereby presented for point mutations in Escherichia coli DNA replication without considering the postreplicative correction by the DNA mismatch repair system. Rates for correct and false enzymatic and mechanochemical processes are considered for calculation of probabilities for false primary inclusion of deoxynucleotides in the growing DNA chain and for defective verification of the new formed base pair in this chain by the DNA polymerase complex. Formulae for obtaining correct new synthesized DNA strand are given. The probability of no false insertion in the entire helix of length N in a correct new DNA strand is calculated to 0.63 with the 10-5 and 10-2 figures for the probabilities of defective base inclusion and escape rate and 4.6106 bp length of the K12 strain E. coli chromosome. Perspectives of reliability analysis for mechanism concerning specificity in biologic processes are discussed.

Xanthine-based molecules such as serine protease dipeptidyl peptidase 4 (DPP4) inhibitors are compounds often used in improving glycemic control in type 2 diabetic patients and also used for their effects as mild stimulants and as bronchodilators, notably in treating asthma symptoms. Here, we aim to better understand the molecular features affecting activity of xanthine-based DPP4 inhibitors such as sitagliptin and related compounds and use these features to de novo predict improved sitagliptin derivatives. To this end, we performed a clinical study to examine the efficacy and safety of once-daily 100 mg oral sitagliptin as monotherapy in Romanian patients with type 2 diabetes. This study indicates that sitagliptin effectively decreases the glycemic level and provides very good glycemic equilibrium. To predict putative new drugs with identical pharmacological effects at lower dosages, we generate QSAR models based on compound series containing 35 DPP4 inhibitors. We establish that the physicochemical parameters critical for DPP4 inhibitory activity are: hydrophobicity described by the logarithm of the octanol/water partition coefficient, counts of rotatable bonds, hydrogen bond donor and acceptor atoms, and topological polar surface area. The predictive power of our QSAR models is indicated by significant values of statistical coefficients: cross-validated correlation q2 (0.77), fitted correlation coefficient r2 (0.85) and standard error of prediction (0.34). Based on the established QSAR equations, we propose and analyse 19 new sitagliptin derivatives with possibly improved pharmacological effect as DPP4 inhibitors.

International audience; Bone is a dynamic tissue that remodels continuously in response to local mechanical and chemical stimuli. This process can also result in maladaptive ectopic bone in response to injury, yet pathological differences at the molecular and structural levels are poorly understood. A number of in vivo models exist but can often be too complex to allow isolation of factors which may stimulate disease progression. A self-structuring model of bone formation is presented using a fibrin gel cast between two calcium phosphate ceramic anchors. Femoral periosteal cells, seeded into these structures, deposit an ordered matrix that closely resembles mature bone in terms of chemistry (collagen:mineral ratio) and structure, which is adapted over a period of one year in culture. Raman spectroscopy and X-ray diffraction confirm that the mineral is hydroxyapatite associated with collagen. Second-harmonic imaging demonstrates that collagen is organized similarly to mature mouse femora. Remarkably, cells differentiated to the osteocyte phase are linked by canaliculi (as demonstrated with nano-computed tomography) and remained viable over the full year of culture. It is demonstrated that novel drugs can prevent ossification in constructs. This model can be employed to study bone formation in an effort to encourage or prevent ossification in a range of pathologies.

International audience; X-ray phase contrast imaging offers higher sensitivity compared to conventional X-ray attenuation imaging and can be simply implemented by propagation when using a partially coherent synchrotron beam. We address the phase retrieval in in-line phase nano-CT using multiple propagation distances. We derive a method which extends Paganin's single distance method and compare it to the contrast transfer function (CTF) approach in the case of a homogeneous object. The methods are applied to phase nano-CT data acquired at the voxel size of 30 nm (ID16A, ESRF, Grenoble, France). Our results show a gain in image quality in terms of the signal-to-noise ratio and spatial resolution when using four distances instead of one. The extended Paganin's method followed by an iterative refinement step provides the best reconstructions while the homogeneous CTF method delivers quasi comparable results for our data, even without refinement step.

In bone remodeling, maturation of the newly formed osteonal tissue is associated with a rapid primary increase followed by a slower secondary increase of mineralization. This requires supply and precipitation of mineral into the bone matrix. Mineral delivery can occur only from the extracellular fluid via interfaces such as the Haversian system and the osteocyte pore network. We hypothesized that in mineralization, mineral exchange is achieved by the diffusion of mineral from the lacunar-canalicular network (LCN) to the bone matrix, resulting in a gradual change in tissue mineralization with respect to the distance from the pore-matrix interface. We expected to observe alterations in the mass density distribution with tissue age. We further hypothesized that mineral exchange occurs not only at the lacunar but also at the canalicular boundaries. The aim of this study was, therefore, to investigate the spatial distribution of mass density in the perilacunar and pericanalicular bone matrix and to explore how these densities are influenced by tissue aging. This is achieved by analyzing human jawbone specimens originating from four healthy donors and four treated with high-dosage bisphosphonate using synchrotron radiation phase-contrast nano-CT with a 50-nm voxel size. Our results provide the first experimental evidence that mass density in the direct vicinity of both lacunae (p

There have been great efforts on the nanoscale 3D probing of brain tissues to image subcellular morphologies. However, limitations in terms of tissue coverage, anisotropic resolution, stain dependence, and complex sample preparation all hinder achieving a better understanding of the human brain functioning in the subcellular context. Herein, X-ray nanoholotomography is introduced as an emerging synchrotron radiation-based technology for large-scale, label-free, direct imaging with isotropic voxel sizes down to 25 nm, exhibiting a spatial resolution down to 88 nm. The procedure is nondestructive as it does not require physical slicing. Hence, it allows subsequent imaging by complementary techniques, including histology. The feasibility of this 3D imaging approach is demonstrated on human cerebellum and neocortex specimens derived from paraffin-embedded tissue blocks. The obtained results are compared to hematoxylin and eosin stained histological sections and showcase the ability for rapid hierarchical neuroimaging and automatic rebuilding of the neuronal architecture at the level of a single cell nucleolus. The findings indicate that nanoholotomography can complement microscopy not only by large isotropic volumetric data but also by morphological details on the sub-100 nm level, addressing many of the present challenges in brain tissue characterization and probably becoming an important tool in nanoanatomy.